Analysis of the algorithm: From kernels to backup genes.

Kernelization section

The algorithm transformed the semantic similarity matrix to make it compatible with a kernel. Once this was done for each network and kernel type, it was integrated by kernel type. Below there is a general analysis of the properties of each matrix in the different phases of the process.

Annotations properties

Table 1. Annotation files descriptors

Net Min Max Average Standard_Deviation
biological_process 1 134 6.999882332176266 11.432654770656663
cellular_component 1 40 4.162222345933308 5.25157343549579
disease 1 21 2.2250479846449136 2.909050012799259
interaction 1.0 729.0 29.8386134923593 54.03869234947398
molecular_function 1 26 3.0287856936832998 3.7159142158779024
pathway 1.0 191.0 4.003825833485152 8.704590940604282
phenotype 1 335 31.553476462477843 46.99329427183839

Matrix properties

Table 2. Similarity matrixes

Net Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
biological_process_sim 16997x16997 288898009 262330240
cellular_component_sim 17963x17963 322669369 322651406
disease_sim 4168x4168 17372224 16578192
genetic_interaction_sim 17354x17354 301161316 59571392
interaction_sim 16098x16098 259145604 479348
molecular_function_sim 17335x17335 300502225 300484890
pathway_sim 3828x3828 14653584 159182
phenotype_sim 5077x5077 25775929 25770852
protein_interaction_sim 16098x16098 259145604 479348

Table 3. Filtered similarity matrixes

Table 4. Uncombined kernel matrixes

Net Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
biological_process ct 16997x16997 288898009 288898009
biological_process el 16997x16997 288898009 288898009
biological_process ka 16997x16997 288898009 262347237
biological_process rf 16997x16997 288898009 288898009
cellular_component ct 17963x17963 322669369 322669369
cellular_component el 17963x17963 322669369 322669369
cellular_component ka 17963x17963 322669369 322669369
cellular_component rf 17963x17963 322669369 322669369
disease ct 4168x4168 17372224 17372224
disease el 4168x4168 17372224 17355558
disease ka 4168x4168 17372224 16582360
disease rf 4168x4168 17372224 17355558
genetic_interaction ct 17354x17354 301161316 301161316
genetic_interaction el 17354x17354 301161316 301161316
genetic_interaction ka 17354x17354 301161316 59588746
genetic_interaction rf 17354x17354 301161316 301161316
molecular_function ct 17335x17335 300502225 300502225
molecular_function el 17335x17335 300502225 300502225
molecular_function ka 17335x17335 300502225 300502225
molecular_function rf 17335x17335 300502225 300502225
pathway ct 3828x3828 14653584 14432317
pathway el 3828x3828 14653584 8641524
pathway ka 3828x3828 14653584 163010
pathway rf 3828x3828 14653584 8641524
phenotype ct 5077x5077 25775929 25775929
phenotype el 5077x5077 25775929 25775929
phenotype ka 5077x5077 25775929 25775929
phenotype rf 5077x5077 25775929 25775929
protein_interaction ct 16098x16098 259145604 259081193
protein_interaction el 16098x16098 259145604 252047984
protein_interaction ka 16098x16098 259145604 495446
protein_interaction rf 16098x16098 259145604 252047984

Table 5. Integrated kernel matrixes

Integration Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
integration_mean_by_presence ct 19629x19629 385297641 374527706
integration_mean_by_presence el 19629x19629 385297641 373497076
integration_mean_by_presence ka 19629x19629 385297641 353862840
integration_mean_by_presence rf 19629x19629 385297641 373497076
mean ct 19629x19629 385297641 374527706
mean el 19629x19629 385297641 373497076
mean ka 19629x19629 385297641 353862840
mean rf 19629x19629 385297641 373497076

Weight values